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Amy Keating, Ph.D.

Assistant Professor of Biology

Room 68-622
617-452-3398 (phone)


A.B. Physics, Harvard, 1992
Ph.D. Chemistry, University of California, Los Angeles, 1998
Helen Hay Whitney Postdoctoral Fellow, Whitehead Institute and MIT Dept. of Chemistry, 1998
Assistant Professor, Dept. of Biology, 2002

Research Summary

Research in the Keating lab is focused on understanding the molecular basis of protein interaction specificity and linking this to biological function. We use a variety of approaches to address this problem, including bioinformatics, molecular modeling, computational protein design and experimental biochemistry and biophysics. The Keating lab is located in the Koch Building (Building 68), where six graduate students, two postdocs and one research technician carry out a variety of computational and experimental studies in adjoining wet and dry labs. The graduate students in the lab come from the Biology and Chemistry departments, and the postdocs are trained in chemistry, biology and computer science. The group makes extensive use of CSBi computational resources and biophysical instrumentation.

Research in Computational and Systems Biology

  • Computational Protein Design
  • Bioinformatics
  • High-throughput assays for protein-protein interactions

Complex networks of protein-protein interactions mediate all cellular processes; it is important to study these networks at many levels of detail. At the highest resolution, network topologies are determined by the interaction specificities of individual proteins. Research in the Keating lab is focused on developing computational methods for predicting and modifying protein interaction specificity, and on developing and applying medium- to high-throughput methods for measuring interaction specificity experimentally.

Because many protein interactions are mediated by discrete modules, the lab targets well-defined interaction motifs such as the alpha-helical coiled coil. A module-based approach provides computational advantages and also simplifies experimental tests. In work on coiled coils, the lab has used a protein microarray approach to measure a large number of interactions between human bZIP transcription factors. These data are a valuable resource that can be used for testing and improving computational methods.

Selected Publications

  • McDonnell, A.V., Jiang, T., Keating, A.E., Berger, B. (2006) śPaircoil2: Improved Prediction of Coiled Coils from Sequence?, Bioinformatics in press
  • Grigoryan, G., Keating, A.E. (2006) Structure-based prediction of bZIP Interaction Specificity?, J. Mol. Bio. 355, 1125.
  • Zhou, F., Grigoryan, G., Lustig, S.R., Keating, A.E., Ceder, G.; Morgan, D (2005) śCoarse-graining protein energetics in sequence variables,? Physical Review Letters 95, 148103.
  • Jiang, T., Keating, A.E. (2005)VID: An integrative framework for discovering functional relationships among proteins,? BMC Bioinformatics 6, 136.
  • Fong, J.H., Keating, A.E., Singh, M.S. (2004) "Predicting specificity in bZIP coiled-coil protein interactions," Genome Biology 5, R11 Newman, J.R.S., Keating, A.E. (2003).
  • "Comprehensive identification of human bZIP interactions with protein microarrays," Science 300, 2097.
  • Keating, A.E., Malashkevich, V.N., Tidor, B., Kim, P.S. (2001) "Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils," Proc. Natl. Acad. Sci. U.S.A. 98, 14825.

Last Updated: April 16, 2008